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- PDB-5ezs: Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein... -

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Basic information

Entry
Database: PDB / ID: 5ezs
TitleVenezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited by E64d
ComponentsNon-structural Protein 2 Cysteine Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Papain-like Cysteine protease / Clan CN / E64d adduct / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Alphavirus nsP2 protease domain / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / : / Non-structural protein 3, zinc-binding domain ...Alphavirus nsP2 protease domain / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Cathepsin B; Chain A / Vaccinia Virus protein VP39 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E6D / Polyprotein P1234
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLegler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CBCall4-CBM-05-2-0019 United States
CitationJournal: Biochemistry / Year: 2016
Title: Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease.
Authors: Hu, X. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Lee, M.S. / Cheung, J. / Ye, W. / Ferrer, M. / Southall, N. / Jadhav, A. / Morazzani, E.M. / Glass, P.J. / Marugan, J. / Legler, P.M.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Non-polymer description
Revision 1.3Jan 17, 2018Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural Protein 2 Cysteine Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6862
Polymers38,3421
Non-polymers3441
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14880 Å2
Unit cell
Length a, b, c (Å)60.890, 63.630, 86.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural Protein 2 Cysteine Protease


Mass: 38341.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain Trinidad donkey)
Strain: Trinidad donkey / Plasmid: pET32a / Production host: Escherichia coli (E. coli)
References: UniProt: P27282, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-E6D / ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate


Mass: 344.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: JCSG+ Condition #8 (0.2 M Ammonium formate, 20% PEG 3350)

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.16→60.89 Å / Num. obs: 18605 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.0591 / Net I/σ(I): 14.16
Reflection shellResolution: 2.16→2.26 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.2655 / Mean I/σ(I) obs: 4.91 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HWK

2hwk


Resolution: 2.16→51.31 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22702 906 4.9 %RANDOM
Rwork0.18976 ---
obs0.19161 17649 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.16→51.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 23 208 2782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192668
X-RAY DIFFRACTIONr_bond_other_d00.022549
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9593627
X-RAY DIFFRACTIONr_angle_other_deg3.70335857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67423.033122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4771521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213018
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.6671293
X-RAY DIFFRACTIONr_mcbond_other0.6861.6651292
X-RAY DIFFRACTIONr_mcangle_it1.2542.4961619
X-RAY DIFFRACTIONr_mcangle_other1.2542.4981620
X-RAY DIFFRACTIONr_scbond_it0.6251.7851375
X-RAY DIFFRACTIONr_scbond_other0.6241.7861376
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1032.6352007
X-RAY DIFFRACTIONr_long_range_B_refined3.38313.6023111
X-RAY DIFFRACTIONr_long_range_B_other3.21313.4113035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.159→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 69 -
Rwork0.219 1213 -
obs--95.17 %

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